It replaces openmm-polymer https://github.com/mirnylab/openmm-polymer-legacy
Documentation is here https://polychrom.readthedocs.io/en/latest/
Compared to openmm-polymer, it has a new storage format described here: https://github.com/mirnylab/polychrom/blob/master/examples/storage_formats/hdf5_reporter.ipynb
New loop extrusion example code is here: https://github.com/mirnylab/polychrom/tree/master/examples/loopExtrusion . It is a good starting point for loop extrusion simulations.
Simplest example simulation that does nothing, which is a good starting point for novel simulations: https://github.com/mirnylab/polychrom/blob/master/examples/example/example.py
For backwards compatibility with analysis routines, we have legacy reporter https://github.com/mirnylab/polychrom/blob/master/examples/storage_formats/legacy_reporter.ipynb and polychrom.polymerutils.load function that is backwards compatible with both new and old style format. https://github.com/mirnylab/polychrom/blob/master/polychrom/polymerutils.py#L22